[med-svn] r5800 - trunk/packages/blat/trunk/debian

Charles Plessy plessy at alioth.debian.org
Sun Jan 30 01:11:26 UTC 2011 

Author: plessy
Date: 2011-01-30 01:11:15 +0000 (Sun, 30 Jan 2011)
New Revision: 5800

Added:
   trunk/packages/blat/trunk/debian/upstream-metadata.yaml
Removed:
   trunk/packages/blat/trunk/debian/README.Debian
   trunk/packages/blat/trunk/debian/reference
Modified:
   trunk/packages/blat/trunk/debian/changelog
   trunk/packages/blat/trunk/debian/control
   trunk/packages/blat/trunk/debian/copyright
Log:
Found a slightly more recent version on my hard drive?\226?\128?\166


Deleted: trunk/packages/blat/trunk/debian/README.Debian
===================================================================
--- trunk/packages/blat/trunk/debian/README.Debian	2011-01-30 01:07:05 UTC (rev 5799)
+++ trunk/packages/blat/trunk/debian/README.Debian	2011-01-30 01:11:15 UTC (rev 5800)
@@ -1,6 +0,0 @@
-blat for Debian
----------------
-
-<possible notes regarding this package - if none, delete this file>
-
- -- Charles Plessy <plessy at debian.org>  Thu, 09 Apr 2009 17:20:01 +0900

Modified: trunk/packages/blat/trunk/debian/changelog
===================================================================
--- trunk/packages/blat/trunk/debian/changelog	2011-01-30 01:07:05 UTC (rev 5799)
+++ trunk/packages/blat/trunk/debian/changelog	2011-01-30 01:11:15 UTC (rev 5800)
@@ -1,4 +1,4 @@
-blat (34-1) unstable; urgency=low
+blat (34-1) UNRELEASED; urgency=low
 
   * Initial release (Closes: #nnnn)  <nnnn is the bug number of your ITP>
 

Modified: trunk/packages/blat/trunk/debian/control
===================================================================
--- trunk/packages/blat/trunk/debian/control	2011-01-30 01:07:05 UTC (rev 5799)
+++ trunk/packages/blat/trunk/debian/control	2011-01-30 01:11:15 UTC (rev 5800)
@@ -1,13 +1,34 @@
 Source: blat
 Section: non-free/science
 Priority: optional
-Maintainer: Charles Plessy <plessy at debian.org>
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy at debian.org>
 Build-Depends: cdbs, debhelper (>= 7)
 Standards-Version: 3.8.1
-Homepage: <insert the upstream URL, if relevant>
+Homepage: http://www.kentinformatics.com/products.html
 
 Package: blat
 Architecture: i386 amd64
 Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: standalone BLAT fast sequence search command line tool
- 
+Description: The BLAST-Like Alignment Tool
+ BLAT on DNA is designed to quickly find sequences of 95% and greater
+ similarity of length 25 bases or more. It may miss more divergent or shorter
+ sequence alignments. It will find perfect sequence matches of 25 bases, and
+ sometimes find them down to 20 bases. BLAT on proteins finds sequences of 80%
+ and greater similarity of length 20 amino acids or more. In practice DNA BLAT
+ works well on primates, and protein blat on land vertebrates.
+ .
+ BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome in
+ memory. The index consists of all non-overlapping 11-mers except for those
+ heavily involved in repeats. The index takes up a bit less than a gigabyte of
+ RAM. The genome itself is not kept in memory, allowing BLAT to deliver high
+ performance on a reasonably priced Linux box. The index is used to find areas
+ of probable homology, which are then loaded into memory for a detailed
+ alignment. Protein BLAT works in a similar manner, except with 4-mers rather
+ than 11-mers. The protein index takes a little more than 2 gigabytes.
+ .
+ BLAT was written by Jim Kent. Like most of Jim's software, interactive use on
+ this web server is free to all. Sources and executables to run batch jobs on
+ your own server are available free for academic, personal, and non-profit
+ purposes. Non-exclusive commercial licenses are also available.

Modified: trunk/packages/blat/trunk/debian/copyright
===================================================================
--- trunk/packages/blat/trunk/debian/copyright	2011-01-30 01:07:05 UTC (rev 5799)
+++ trunk/packages/blat/trunk/debian/copyright	2011-01-30 01:11:15 UTC (rev 5800)
@@ -1,8 +1,7 @@
-Name: BLAT
-Contact: Jim Kent <jim_kent at pacbell.net>
-Source:
+Format: DEP-5
+Source: http://users.soe.ucsc.edu/~kent/src/blatSrc34.zip
 
-License:
+License: BLAT
  This archive contains the entire source tree for BLAT and
  associated utilities.  All files are copyrighted, but license 
  is hereby granted for personal, academic, and non-profit use.  
@@ -12,5 +11,25 @@
 
 Files: debian/*
 Copyright: 2009, Charles Plessy <plessy at debian.org>
-License: PD
- Please treat the packaging work as if it were public domain.
+License: BOLA-1.1
+ BOLA - Buena Onda License Agreement (v1.1)
+ ------------------------------------------
+ .
+ This work is provided 'as-is', without any express or implied warranty. In no
+ event will the authors be held liable for any damages arising from the use of
+ this work.
+ .
+ To all effects and purposes, this work is to be considered Public Domain.
+ .
+ .
+ However, if you want to be "buena onda", you should:
+ .
+  1. Not take credit for it, and give proper recognition to the authors.
+  2. Share your modifications, so everybody benefits from them.
+  3. Do something nice for the authors.
+  4. Help someone who needs it: sign up for some volunteer work or help your
+     neighbour paint the house.
+  5. Don't waste. Anything, but specially energy that comes from natural
+     non-renewable resources. Extra points if you discover or invent something
+     to replace them.
+  6. Be tolerant. Everything that's good in nature comes from cooperation.

Deleted: trunk/packages/blat/trunk/debian/reference
===================================================================
--- trunk/packages/blat/trunk/debian/reference	2011-01-30 01:07:05 UTC (rev 5799)
+++ trunk/packages/blat/trunk/debian/reference	2011-01-30 01:11:15 UTC (rev 5800)
@@ -1,12 +0,0 @@
- at article{W. JamesKent04012002,
-author = {Kent, W. James},
-title={{BLAT—The BLAST-Like Alignment Tool}},
-journal = {Genome Research},
-volume = {12},
-number = {4},
-pages = {656-664},
-doi = {10.1101/gr.229202},
-year = {2002},
-URL = {http://genome.cshlp.org/content/12/4/656.abstract},
-eprint = {http://genome.cshlp.org/content/12/4/656.full.pdf+html}
-}

Added: trunk/packages/blat/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/blat/trunk/debian/upstream-metadata.yaml	                        (rev 0)
+++ trunk/packages/blat/trunk/debian/upstream-metadata.yaml	2011-01-30 01:11:15 UTC (rev 5800)
@@ -0,0 +1,12 @@
+NAME: BLAT
+Reference:
+ author = Kent, W. James
+ title = BLAT—The BLAST-Like Alignment Tool
+ journal = Genome Research
+ volume = 12
+ number = 4
+ pages = 656-664
+ doi = 10.1101/gr.229202
+ year = 2002
+ URL = http://genome.cshlp.org/content/12/4/656.abstract
+ eprint = http://genome.cshlp.org/content/12/4/656.full.pdf+html

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